If you want traditional food in Bologna, then I think the best place is this one:
Via Santa Caterina, 51
it's a bit difficult to find but it's well worth a visit. You get traditional dishes done correctly and with great produce. Their wine list is good too. Last time I've been there was about 3 years ago, if I recall right it costed about 45 euro plus wine. Beware you need to book it with a good advance.
If you can use a car and got in the outsides of Bologna, then I heard great comments about Berberè and their pizza. You need to book in advance and be prepared for a slooow service.
If you are interested in pastry shops and you can use a car, then a visit to Gino Fabbri is mandatory, he is one of the best 5 pastry chefs in Italy in my opinion. Only problem is that you need a car and a navigator to reach his shop, it's in a village outside Bologna. Once there you just need to choose what you prefer, I tried a lot of his stuff and it ranged from really good to excellent.
Another very good pastry shop is Regina di Quadri, this is easier to reach since it's within the "exagon" in the center of Bologna.
I'll ask to some friends living there for more suggestions.
All the websites I linked don't have an English version (major defect of most food related websites in Italy), if you need help feel free to ask.